Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production

Abstract

Egg production is an important economic trait and a key indicator of reproductive performance in ducks. Egg production is regulated by several factors including genes. However the genes involved in egg production in duck remain unclear. In this study, we compared the ovarian transcriptome of high egg laying (HEL) and low egg laying (LEL) ducks using RNA-Seq to identify the genes involved in egg production. The HEL ducks laid on average 433 eggs while the LEL ducks laid 221 eggs over 93 weeks. A total of 489 genes were found to be significantly differentially expressed out of which 310 and 179 genes were up and downregulated, respectively, in the HEL group. Thirty-eight differentially expressed genes (DEGs), including LHX9, GRIA1, DBH, SYCP2L, HSD17B2, PAR6, CAPRIN2, STC2, and RAB27B were found to be potentially related to egg production and folliculogenesis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that DEGs were enriched for functions related to glutamate receptor activity, serine-type endopeptidase activity, immune function, progesterone mediated oocyte maturation and MAPK signaling. Protein–protein interaction network analysis (PPI) showed strong interaction between 32 DEGs in two distinct clusters. Together, these findings suggest a mix of genetic and immunological factors affect egg production, and highlights candidate genes and pathways, that provides an understanding of the molecular mechanisms regulating egg production in ducks and in birds more broadly.

Identification of differentially expressed genes and signaling pathways in Gaoyou duck ovary at different physiological stages

“…An increasing body of evidence suggests that the MAPK (mitogen-activated protein kinase) signaling pathway participates in cell proliferation, differentiation of apoptosis, and the reproductive process ( 17 ). A recent study identified that the MAPK signaling pathway was involved in the egg production and folliculogenesis of Indian domestic ducks ( 4 ). The actin cytoskeleton signaling pathway is involved in cellular functions ( 18 ).…”

“…In recent years, the ovarian tissues of high- and low-egg-production individuals of poultries, including ducks, geese, and chicken, have been studied through RNA-Seq, which provides a convenient way to explore the candidate genes related to egg-laying performance. Karippadakam et al ( 4 ) compared the high and low egg-laying ovarian transcriptome of Indian domestic ducks and found 38 DEGs potentially related to egg production performance. Kun et al ( 5 ) conducted a comparative study on high and low egg-laying Leizhou black ducks using ovary tissue, revealing two key signaling pathways, steroid biosynthesis and FSH signal pathway, involved in the egg-laying performance of Leizhou black ducks.…”

Identification of Critical Immune Regulators and Potential Interactions of IL-26 in Riemerella anatipestifer-Infected Ducks by Transcriptome Analysis and Profiling

“…The p-values were adjusted using the Benjamini-Hochberg method for controlling the false discovery rate (FDR), and significantly differentially expressed genes (DEGs) were defined as genes with a p-adjusted FDR < 0.05 and Log 2 |fold change| (Log 2 FC) ≥ 1 [23]. Due to the limited annotations of duck genes, functional clustering and pathway enrichment analysis of DEGs were performed indirectly as described elsewhere, with modifications [24]. First, the duck ensemble gene IDs were converted to their chicken ortholog identifiers using the g:Orth function in g:Profiler (version: e111_eg58_p18_30541362, https://biit.cs.ut.ee/gprofiler/orth, accessed on 19 February 2024), and then the matched gene IDs were used for subsequent analyses.…”

Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks

“…The ovary, as a crucial organ for poultry egg-laying, plays a significant role in egg production [1]. Further research indicates that the process of folliculogenesis in the ovary determines the egg-laying performance of ducks [2]. RNA-seq technology has been applied to study the ovarian transcriptome of individuals with high-and low-egg-laying performances in poultry species, such as chickens, ducks, and geese [3][4][5].…”